R/vsVolcano.R

In vidger: Create rapid visualizations of RNAseq data in R

#' @title
#' Volcano plot from \eqn{log_{2}} fold changes and
#' \eqn{-log_{10}}(\eqn{p}-values)
#'
#' @author
#' Brandon Monier, \email{brandon.monier@sdstate.edu}
#'
#' @description
#' This function allows you to extract necessary results-based data from
#' either a \code{DESeq2} object, \code{edgeR} object, or \code{cuffdiff} data
#' frame to create a volcano plot (i.e. a scatter plot) of the negative
#' \eqn{log} of the \eqn{p}-value versus the \eqn{log} of the fold change
#' while implementing ggplot2 aesthetics.
#'
#' @param x treatment \code{x} for comparison (\eqn{log_{2}}(x/control)). This
#'  will be a factor level in your data.
#' @param y treatment \code{y} for comparison (\eqn{log_{2}}(y/control)). This
#'  will be a factor level in your data.
#' @param data output generated from calling the main routines of either
#'  \code{cuffdiff}, \code{DESeq2}, or \code{edgeR} analyses. For
#'  \code{cuffdiff}, this will be a \code{*_exp.diff} file. For \code{DESeq2},
#'  this will be a generated object of class \code{DESeqDataSet}. For
#'  \code{edgeR}, this will be a generated object of class \code{DGEList}.
#' @param d.factor a specified factor; for use with \code{DESeq2} objects only.
#'  This input equates to the first parameter for the contrast argument when
#'  invoking the \code{results()} function in \code{DESeq2}. Defaults to
#'  \code{NULL}.
#' @param type an analysis classifier to tell the function how to process the
#'  data. Must be either \code{cuffdiff}, \code{deseq}, or \code{edger}.
#'  \code{cuffdiff} must be used with \code{cuffdiff} data; \code{deseq} must
#'  be used for \code{DESeq2} output; \code{edgeR} must be used with
#'  \code{edgeR} data. See the \code{data} parameter for further details.
#' @param padj a user defined adjusted \eqn{p}-value cutoff point.
#'  Defaults to \code{0.05}.
#' @param x.lim set manual limits (boundaries) to the x axis. Defaults to
#'  \code{NULL}.
#' @param lfc \eqn{log} fold change level for setting conditonals. If no user
#'  input is added (\code{NULL}), value defaults to \code{1}.
#' @param title display the main title of plot. Logical; defaults to
#'  \code{TRUE}. If set to \code{FALSE}, no title will display in plot.
#' @param legend display legend of plot. Logical; defaults to \code{TRUE}.
#'  If set to \code{FALSE}, no legend will display in plot.
#' @param grid display major and minor axis lines. Logical; defaults to
#'  \code{TRUE}. If set to \code{FALSE}, no axis lines will display in plot.
#' @param highlight character string of IDs that will be highlighted. Set to
#'  \code{NULL} if you do not want highlighted data.
#' @param data.return returns data output of plot Logical; defaults to
#'  \code{FALSE}. If set to \code{TRUE}, a data frame will also be called.
#'  Assign to object for reproduction and saving of data frame. See final
#'  example for further details.
#' @param xaxis.title.size change the font size of the \code{x}-axis title
#'  text. Defaults to \code{10}.
#' @param xaxis.text.size change the font size of the \code{x}-axis text.
#'  Defaults to \code{10}.
#' @param yaxis.title.size change the font size of the \code{y}-axis title
#'  text. Defaults to \code{10}.
#' @param yaxis.text.size change the font size of the \code{y}-axis text.
#'  Defaults to \code{10}.
#' @param main.title.size change the font size of the plot title text.
#'  Defaults to \code{15}.
#' @param legend.text.size change the font size of the legend body text.
#'  Defaults to \code{9}.
#'
#' @return An object created by \code{ggplot}
#'
#' @export
#'
#' @examples
#' # Cuffdiff example
#' data("df.cuff")
#' vsVolcano(
#'      x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL,
#'      type = "cuffdiff", padj = 0.05, x.lim = NULL, lfc = 2,
#'      title = TRUE, grid = TRUE, data.return = FALSE
#' )
#'
#' # DESeq2 example
#' data("df.deseq")
#' require(DESeq2)
#' vsVolcano(
#'      x = "treated_paired.end", y = "untreated_paired.end",
#'      data = df.deseq, d.factor = "condition",
#'      type = "deseq", padj = 0.05, x.lim = NULL, lfc = NULL,
#'      title = TRUE, grid = TRUE, data.return = FALSE
#' )
#'
#' # edgeR example
#' data("df.edger")
#' require(edgeR)
#' vsVolcano(
#'      x = "WM", y = "MM", data = df.edger, d.factor = NULL,
#'      type = "edger", padj = 0.1, x.lim = NULL, lfc = 2,
#'      title = FALSE, grid = TRUE, data.return = FALSE
#' )
#'
#  #Highlight IDs
#' data("df.deseq")
#' require(DESeq2)
#' hl <- c(
#'     "FBgn0036248",
#'     "FBgn0026573",
#'     "FBgn0259742",
#'     "FBgn0038961",
#'     "FBgn0038928"
#' )
#' vsVolcano(
#'     x = "treated_paired.end", y = "untreated_paired.end",
#'     data = df.deseq, d.factor = "condition",
#'     type = "deseq", padj = 0.05, x.lim = NULL, lfc = NULL,
#'     title = TRUE, grid = TRUE, data.return = FALSE, highlight = hl
#' )
#'
#' # Extract data frame from visualization
#' data("df.cuff")
#' tmp <- vsVolcano(
#'      x = "hESC", y = "iPS", data = df.cuff,
#'      d.factor = NULL, type = "cuffdiff", padj = 0.05,
#'      x.lim = NULL, lfc = 2, title = TRUE, grid = TRUE,
#'      data.return = TRUE
#' )
#' df_volcano <- tmp[[1]] ## or use tmp$data
#' head(df_volcano)
#'
#' # Show plot from object (see prior example for more details)
#' tmp[[2]] ## or use tmp$plot

vsVolcano <- function(
    x, y, data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"),
    padj = 0.05, x.lim = NULL, lfc = NULL, title = TRUE, legend = TRUE,
    grid = TRUE, highlight = NULL, data.return = FALSE, xaxis.text.size = 10,
    yaxis.text.size = 10, xaxis.title.size = 10, yaxis.title.size = 10,
    main.title.size = 15, legend.text.size = 9
) {
    if (missing(type) || !type %in% c("cuffdiff", "deseq", "edger")) {
        stop(
            paste(
                "Please specify analysis type",
                "(\"cuffdiff\", \"deseq\", or \"edger\")"
            )
        )
    }


    type <- match.arg(type)
    if (type == "cuffdiff") {
        dat <- .getCuffVolcano(x, y, data)
    } else if (type == "deseq") {
        dat <- .getDeseqVolcano(x, y, data, d.factor)
    } else if (type == "edger") {
        dat <- .getEdgeVolcano(x, y, data)
    }

    if (!isTRUE(title)) {
        m.lab <- NULL
    } else {
        m.lab  <- ggtitle(paste(y, "vs.", x))
    }

    if (!isTRUE(legend)) {
        leg <- theme(legend.position = "none")
    } else {
        leg <- guides(
            colour = guide_legend(override.aes = list(size = 3)),
            shape = guide_legend(override.aes = list(size = 3))
        )
    }

    if (!isTRUE(grid)) {
        grid <- theme_classic()
    } else {
        grid <- theme_bw()
    }

    dat$isDE <- ifelse(dat$padj < padj, TRUE, FALSE)
    px <- dat$logFC
    p <- padj

    if (is.null(x.lim)) {
        x.lim = c(-1, 1) * quantile(abs(px[is.finite(px)]), probs = 0.99)
    }

    if (is.null(lfc)) {
        lfc = 1
    }

    dat <- .vo.ranker(dat, padj, lfc, x.lim)

    tmp.size <- .vo.out.ranker(px, x.lim[2])
    tmp.col <- .vo.col.ranker(dat$isDE, px, lfc)
    tmp.shp <- .vo.shp.ranker(px, x.lim)

    tmp.cnt <- .vo.col.counter(dat, lfc)
    b <- tmp.cnt[[1]]
    g <- tmp.cnt[[2]]

    comp1 <- .vo.comp1(x.lim, padj, lfc, b, g)
    point <- geom_point(
        alpha = 0.7,
        aes(color = tmp.col, shape = tmp.shp, size = tmp.size)
    )
    comp2 <- .vo.comp2(
        comp1[[4]], comp1[[6]], comp1[[5]], comp1[[1]], comp1[[2]], comp1[[3]]
    )

    text.size <- theme(
        axis.text.x = element_text(size = xaxis.text.size),
        axis.text.y = element_text(size = yaxis.text.size),
        axis.title.x = element_text(size = xaxis.title.size),
        axis.title.y = element_text(size = yaxis.title.size),
        plot.title = element_text(size = main.title.size),
        legend.text = element_text(size = legend.text.size)
    )

    id <- logFC <- NULL
    if (is.null(highlight)) {
        tmp.plot <- ggplot(
            dat, aes(x = pmax(x.lim[1], pmin(x.lim[2], px)), y = -log10(padj) )
        ) +
            point + comp2$color + comp2$shape + comp1$vline1 + comp1$vline2 +
            comp1$vline3 + comp1$x.lab + comp1$y.lab + comp1$hline1 + grid  +
            m.lab + xlim(x.lim) + comp2$size + leg + text.size
    } else {
        tl <- length(setdiff(highlight, dat$id))
        if (!is.atomic(highlight)) {
            stop("\"highlight\" must be vector.")
        } else if (all(highlight %in% dat$id)) {
            hl <- highlight
        } else if (tl > 0 && tl < length(highlight)) {
            remove <- setdiff(highlight, dat$id)
            message("Some IDs not found in data frame:")
            print(remove)
            message("Plotting the remaining samples...")
            hl <- highlight[!highlight %in% remove]
        } else if (!all(highlight %in% dat$id)) {
            stop("No IDs in highlight vector are present in data frame.")
        }

        tmp.plot <- ggplot(
            dat, aes(x = pmax(x.lim[1], pmin(x.lim[2], px)), y = -log10(padj) )
        ) +
            geom_point(
                alpha = 0.4,
                aes(color = tmp.col, shape = tmp.shp, size = tmp.size)
            ) +
            comp2$color + comp2$shape + comp1$vline1 + comp1$vline2 +
            comp1$vline3 + comp1$x.lab + comp1$y.lab + comp1$hline1 +
            comp2$size  + m.lab + xlim(x.lim) +
            ggrepel::geom_label_repel(
                data = dat[which(dat$id %in% hl), ],
                aes(label = id, x = logFC, y = padj),
                segment.size = 1,
                segment.color = "gray10",
                box.padding = unit(0.4, "lines"),
                point.padding = unit(0.4, "lines")
            ) +
            geom_point(
                data = dat[which(dat$id %in% hl), ],
                aes(x = logFC, y = padj),
                color = "red",
                size = 3
            ) +
            grid + leg + text.size
    }

    if (isTRUE(data.return)) {
        dat2 <- dat[, -ncol(dat)]
        plot.l <- list(data = dat2, plot = tmp.plot)
    } else {
        print(tmp.plot)
    }
}